15-68304789-T-C

Position:

• chr15-68304789-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004439.2(ITGA11):​c.3382-904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,038 control chromosomes in the GnomAD database, including 10,051 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (10051 hom., cov: 32)
• Consequence: ITGA11 NM_001004439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45

Genes affected

ITGA11 (HGNC:6136): (integrin subunit alpha 11) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein contains an I domain, is expressed in muscle tissue, dimerizes with beta 1 integrin in vitro, and appears to bind collagen in this form. Therefore, the protein may be involved in attaching muscle tissue to the extracellular matrix. Alternative transcriptional splice variants have been found for this gene, but their biological validity is not determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ITGA11	NM_001004439.2	c.3382-904A>G		intron_variant		ENST00000315757.9	NP_001004439.1
ITGA11	XM_005254228.4	c.3076-904A>G		intron_variant			XP_005254285.1
ITGA11	XM_011521363.3	c.3175-904A>G		intron_variant			XP_011519665.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9	c.3382-904A>G		intron_variant		1	NM_001004439.2	ENSP00000327290	P4
ITGA11	ENST00000423218.6	c.3385-904A>G		intron_variant		2		ENSP00000403392	A1

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53128 AN: 151920 Hom.: 10041 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.350 AC: 53179 AN: 152038 Hom.: 10051 Cov.: 32 AF XY: 0.341 AC XY: 25355 AN XY: 74318

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.0346

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.373

Alfa AF: 0.337 Hom.: 11731

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.40

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7174755; hg19: chr15-68597127;